ENST00000518540.5:n.416-28624G>A

Variant names:

• chr8-68982786-C-T
• rs7825569
• ENST00000518540.5:n.416-28624G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000518540.5(LINC01592):​n.416-28624G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 152,038 control chromosomes in the GnomAD database, including 25,290 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.55 (25290 hom., cov: 32)
• Consequence: LINC01592 ENST00000518540.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510
• Publications: 3 publications found

Genes affected

LINC01592 (HGNC:51557): (long intergenic non-protein coding RNA 1592)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01592	NR_039986.1	n.416-28624G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01592	ENST00000518540.5	n.416-28624G>A		intron_variant	Intron 2 of 4	2
LINC01592	ENST00000519062.7	n.149+18598G>A		intron_variant	Intron 1 of 3	3
LINC01592	ENST00000524286.2	n.166+15518G>A		intron_variant	Intron 2 of 4	3

Frequencies

GnomAD3 genomes AF: 0.547 AC: 83147 AN: 151920 Hom.: 25231 Cov.: 32

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.516

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.548 AC: 83267 AN: 152038 Hom.: 25290 Cov.: 32 AF XY: 0.546 AC XY: 40575 AN XY: 74298

African (AFR) AF: 0.827 AC: 34341 AN: 41504

American (AMR) AF: 0.503 AC: 7675 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1513 AN: 3470

East Asian (EAS) AF: 0.491 AC: 2533 AN: 5162

South Asian (SAS) AF: 0.625 AC: 3014 AN: 4820

European-Finnish (FIN) AF: 0.362 AC: 3825 AN: 10564

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.422 AC: 28687 AN: 67942

Other (OTH) AF: 0.513 AC: 1083 AN: 2112

Alfa AF: 0.450 Hom.: 25800

Bravo AF: 0.567

Asia WGS AF: 0.548 AC: 1902 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.34
PhyloP100		-0.051

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7825569; hg19: chr8-69895021;